A fundamental difficulty in protein research is the ability to efficiently extract proteins from SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) gels following electrophoretic separations. Gel electrophoresis separates proteins on the basis of molecular weight and size. An electric field applied across the gel assists in the transit of the proteins through the sieve-like pores of the gel matrix. After the electrophoretic separation is finished, the gels are often “fixed” through a chemical treatment of the gel to prevent the solvated proteins from diffusing within the gel. The fixing solution contains organic solvent (e.g. methanol or ethanol) and acidic modifiers (e.g. acetic or formic acid) that induce a precipitation of the proteins within the gel matrix, which effectively inhibits the proteins from diffusing from their position. Subsequent staining of the fixed proteins with silver or Coomassie stains permits visualization of the separated protein gel bands. While fixation is important for maintaining the resolution of the gel separation over time, the process greatly reduces the ability of downstream chemical analysis of the proteins due to their insoluble nature.
Two common types of sample preparation methods exist for downstream analysis of gel separated proteins: enzymatic digestion for protein identification analyses and extraction of the intact protein. In protein identification experiments, the proteins are digested in-gel using proteolytic enzymes (e.g. trypsin, endoproteinase Glu-C, Arg-C, Lys-C). Following digestion, the resultant peptide mixtures are extracted from the gel matrix for subsequent analysis by HPLC-MS/MS, or chromatographic separation of the peptide mixtures coupled on-line with detection by tandem mass spectrometry, for collection of peptide MS/MS spectra that are used in database correlation analysis for protein identification. Alternatively, the proteins can be extracted intact from the gel matrix and used in a variety of downstream analyses, such as direct infusion mass spectrometry or matrix assisted laser desorption ionization (MALDI) mass spectrometry experiments for determination of molecular weight. In both cases, the precipitated nature of the proteins in fixed gels impedes the collection of the peptide digest mixtures or intact proteins from the gel. Extraction of the samples is achieved through repeated rinses of the gel bands, which heavily relies on diffusion of the analytes into the extraction solution. The precipitated nature of the proteins also impedes digestion by reducing the enzyme activity, as compared to digestion of soluble protein molecules. Effectively, the gel matrix is useful for electrophoretic separation of proteins mixtures, but hampers downstream analysis of the protein analytes.
Currently, techniques for extraction of the proteins from the excised gel band involve repetitive extraction rinses, followed by drying down of the collected rinsed to remove the solvent. Generally, this method relies on diffusion of the protein molecules out of the gel matrix and into the extraction solvent. Because of their large size relative to the dimensions of the gel pores, this technique is very limited for the extraction of intact proteins from the gel matrix. Fixation of the proteins further compounds the problem. Peptide digests can be extracted with greater success due to their smaller size, but the process remains diffusion-limited. Alternatively, excised gel bands have been minced up using homogenizers to increase the surface area of the gel band for extraction. While homogenization improves diffusion-limited extraction, it also introduces potential contamination of the sample and can create ultrafine gel particles that are also collected in the extraction rinses and impede downstream analyses. Additionally, homogenization does not alleviate the solubility problems associated with fixed proteins.
Electroelution is a technique that utilizes the application of an electric field to induce migration of the proteins in a gel band into solution. Conventional methods of extracting gel-separated proteins using electroelution are believed to have been largely unsuccessful and/or non-reproducible for a variety of reasons. Electroelution is most effective for the extraction of solubilized proteins, and chemical fixation of proteins during staining greatly hampers the electroelution process. Electroelution requires the application of an electric field across the excised gel band, and the tiny, asymmetric nature of the gel piece presents inherent problems for fabrication of an electroelution device. After electroelution from the gel piece, proteins are free to adsorb onto surfaces of the electroelution device or on the surface of the gel. Lastly, collection of extracted proteins by such methods can be largely inefficient because the proteins are often diluted into larger volumes of solvent. Adsorption losses during extraction and collection, coupled with transport/handling losses and contamination, can reduce the overall efficiency of the electroelution process and negatively impact the reproducibility.
Accordingly, there is a need for an electroelution process and device to reproducibly and efficiently extract electrophoretically separated intact proteins from an SDS-PAGE gel matrix.
Biological solutions are often comprised of a dilute mixture of the analytes of interest, other similar chemical species, chemical contaminants, and bulk solvent molecules. Sample preparation of these solutions can thus require the concentration of the analytes (i.e., proteins) and purification of the analyte from the mixture. Conventional methods of concentrating the sample solution often utilize a porous membrane filter possessing a characteristic molecular weight cut-off (MWCO). Molecules of a size below the MWCO of the membrane pass through the pores and constitute the filtrate, while molecules of a size above the MWCO of the membrane are retained by the membrane as the retentate. Following concentration of a solution, the retentate can be purified through dilutional rinses using a buffer solution that is free of the chemical contaminants, and re-concentration of the retentate. Additionally, the retentate composition can be changed through solvent exchange rinses and re-concentration of the retentate solution.
While simple in concept, the concentration and purification of protein samples through the use of MWCO ultrafiltration (UF) membranes can be difficult to perform reproducibly and effectively on the bench top. Traditionally, centrifugal tubes containing the MWCO membranes are utilized. The sample solution is loaded onto the membrane surface in the upper retentate reservoir of the centrifugal ultrafiltration tube. A centrifuge is used to provide a gravitational driving force to push the solvent through the membrane filter and into the filtrate reservoir. Membrane fouling is a major problem for these devices, as particles can clog the pores of the membrane, resulting in decreased flow and increased adsorption of species onto the cloggants. Additionally, the recovery yield can be significantly affected, as recovery of sample proteins adsorbed onto the device surfaces and MWCO membrane can be difficult and poorly reproducible. Sample recovery can involve manual pipetting (Pall NanoSep and MicroSep devices ) or inversion of the retentate reservoir and centrifugal collection of the sample (Millipore Ultrafree-MC and -CL devices).
Centrifugal ultrafiltration devices can be run in parallel, as many of the units can be spun in a centrifuge simultaneously. However, these centrifugal UF devices are very labor-intensive, as each step of sample addition, filtrate removal, rinse solution addition, and retentate recovery require manual manipulation of each device. Thus, the cumulative efforts for concentration and purification of a large number of samples can become time and labor intensive, and there can also be increased opportunities for contamination and handling/transfer losses.
Accordingly, there is a need for a sample separation process and device to assist researchers in the concentration, purification, and preparation of protein samples for analysis.